@vibe-agent-toolkit/cli 0.2.0-rc.2 → 0.2.0-rc.3

package/dist/commands/agent/install.js

@@ -30,9 +30,18 @@ export async function installAgent(agentName, options) {
         // Ensure target directory exists
         // eslint-disable-next-line security/detect-non-literal-fs-filename -- Path constructed from validated scope location
         await fs.mkdir(targetLocation, { recursive: true });
-        // Check if already installed
+        // Check if already installed.
+        //
+        // `lstat`, not `access`: `access` FOLLOWS symlinks, so a dangling dev-mode
+        // link — precisely what `build:clean` orphans by deleting `dist/` under a
+        // previous `--dev` install — answered ENOENT here. That fell into the catch
+        // below as "not installed", which skipped the `--force` removal and left the
+        // link in place for `fs.symlink` to reject with EEXIST. `--force` was inert
+        // against the one state it most needed to clear. `lstat` stats the link
+        // itself, so the entry is seen whether or not its target still exists.
         try {
-            await fs.access(installPath);
+            // eslint-disable-next-line security/detect-non-literal-fs-filename -- installPath is built from a validated scope location
+            await fs.lstat(installPath);
             if (!force) {
                 logger.error(`\n${agentName} already installed at ${installPath}\n` +
                     `Use --force to overwrite\n`);
@@ -45,9 +54,7 @@ export async function installAgent(agentName, options) {
             // Not installed, continue
         }
         if (dev) {
-            // Symlink for development
-            // eslint-disable-next-line security/detect-non-literal-fs-filename -- Paths from validated sources
-            await fs.symlink(builtSkillPath, installPath, 'dir');
+            await linkForDevelopment(builtSkillPath, installPath);
             logger.info(`✓ Symlinked ${agentName} to ${installPath} (dev mode)`);
             logger.info(`  Rebuild agent to see changes immediately`);
         }
@@ -64,6 +71,40 @@ export async function installAgent(agentName, options) {
         handleCommandError(error, logger, startTime, 'Install');
     }
 }
+/**
+ * Symlink a built bundle into place for `--dev`, failing legibly where the OS
+ * refuses.
+ *
+ * ⚠️ **This is POSIX-only in practice, and not by anything written here.**
+ * `installAgent` refuses `dev` on win32 before this is reachable, naming WSL
+ * and copy mode. So Windows never gets this far, and any Windows-specific
+ * handling added here would be dead code — an earlier revision added exactly
+ * that, relabelling a `SeCreateSymbolicLinkPrivilege` EPERM that cannot occur.
+ * If `--dev` is ever to work on Windows, the change belongs at that guard (a
+ * junction takes no elevation, as `dev-tools/src/link-workspace-packages.ts`
+ * already does), not in this catch.
+ *
+ * Deliberately does NOT fall back to copying. `--dev` exists so a rebuild is
+ * picked up live; a copy that reported success would leave someone editing
+ * sources and wondering why nothing changes — a silent wrong answer in place of
+ * a loud, correct refusal.
+ *
+ * @param builtSkillPath - Absolute path to the built bundle
+ * @param installPath - Where the link should be created
+ * @throws When the link cannot be created, naming the remedy
+ */
+async function linkForDevelopment(builtSkillPath, installPath) {
+    try {
+        // eslint-disable-next-line security/detect-non-literal-fs-filename, local/no-bare-symlink-in-tests -- eyes open: win32 is refused by the guard in `installAgent` before this runs, so the Windows privilege hazard the rule names cannot be reached here.
+        await fs.symlink(builtSkillPath, installPath, 'dir');
+    }
+    catch (error) {
+        const detail = error instanceof Error ? error.message : String(error);
+        throw new Error(`Could not create the dev-mode symlink at ${installPath}: ${detail}\n` +
+            `Re-run with --force to replace whatever is already at ${installPath}, ` +
+            'or install without --dev to copy the bundle instead of linking it.');
+    }
+}
 /**
  * Find built skill bundle
  */

package/dist/commands/agent/install.js.map

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package/dist/commands/audit/distributed-tree.d.ts

@@ -89,8 +89,8 @@
  * third answer, `'indeterminate'`, and reports it (see
  * {@link distributedTreeFindings}) rather than guessing in either direction.
  */
-import { type ValidationIssue } from '@vibe-agent-toolkit/agent-schema';
 import { type GitTrackerSource } from '@vibe-agent-toolkit/claude-marketplace';
+import { type ValidationIssue } from '@vibe-agent-toolkit/schema';
 import { GitTracker } from '@vibe-agent-toolkit/utils';
 /**
  * Get (or build) the pre-populated tracker for one git root.

package/dist/commands/audit/distributed-tree.d.ts.map

@@ -1 +1 @@
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package/dist/commands/audit/distributed-tree.js.map

@@ -1 +1 @@
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package/dist/commands/audit/hierarchical-output.d.ts

@@ -1,5 +1,5 @@
-import { type ValidationIssue } from '@vibe-agent-toolkit/agent-schema';
 import type { ValidationResult } from '@vibe-agent-toolkit/agent-skills';
+import { type ValidationIssue } from '@vibe-agent-toolkit/schema';
 export interface HierarchicalOutput {
     marketplaces: MarketplaceGroup[];
     cachedPlugins: PluginGroup[];

package/dist/commands/audit/hierarchical-output.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hierarchical-output.d.ts","sourceRoot":"","sources":["../../../src/commands/audit/hierarchical-output.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,kCAAkC,CAAC;AACzE,OAAO,EAGL,KAAK,eAAe,EACrB,MAAM,4BAA4B,CAAC;AAGpC,MAAM,WAAW,kBAAkB;IACjC,YAAY,EAAE,gBAAgB,EAAE,CAAC;IACjC,aAAa,EAAE,WAAW,EAAE,CAAC;IAC7B,iBAAiB,EAAE,WAAW,EAAE,CAAC;IACjC,gBAAgB,EAAE,UAAU,EAAE,CAAC;CAChC;AAED,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,WAAW,EAAE,CAAC;CACxB;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,UAAU,EAAE,CAAC;CACtB;AAED,MAAM,MAAM,WAAW,GAAG,OAAO,GAAG,UAAU,GAAG,OAAO,CAAC;AAEzD,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,0EAA0E;IAC1E,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,OAAO,CAAC;IACxC,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,WAAW,CAAC,EAAE,WAAW,CAAC;CAC3B;AAqaD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,gBAAgB,EAAE,EAC3B,OAAO,EAAE,OAAO,EAChB,YAAY,EAAE,MAAM,GACnB,kBAAkB,CAyCpB"}

package/dist/commands/audit/hierarchical-output.js

@@ -1,5 +1,5 @@
 import * as os from 'node:os';
-import { calculateValidationStatus, countBySeverity, } from '@vibe-agent-toolkit/agent-schema';
+import { calculateValidationStatus, countBySeverity, } from '@vibe-agent-toolkit/schema';
 import { issueLocation, toForwardSlash } from '@vibe-agent-toolkit/utils';
 /** Build {@link ParsedSkillPath.identity} from the parsed segments. */
 function skillIdentity(parts, marketplace, plugin, skill) {

package/dist/commands/audit/hierarchical-output.js.map

@@ -1 +1 @@
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package/dist/commands/audit.d.ts

@@ -2,9 +2,9 @@
  * Audit command - audits plugins, marketplaces, registries, and Agent Skills
  * Top-level command: vat audit [path]
  */
-import { type SeverityCounts } from '@vibe-agent-toolkit/agent-schema';
 import { type SkillPackagingConfig, type ValidationResult } from '@vibe-agent-toolkit/agent-skills';
 import { type CompatibilityResult, type EffectiveSettings } from '@vibe-agent-toolkit/claude-marketplace';
+import { type SeverityCounts } from '@vibe-agent-toolkit/schema';
 import { Command } from 'commander';
 import { createLogger } from '../utils/logger.js';
 export interface AuditCommandOptions {
@@ -98,6 +98,27 @@ export declare function auditCommand(targetPath: string | undefined, options: Au
  *   location reads, or a run spanning several configs emits one document in
  *   several coordinate systems. Recursion passes it through unchanged.
  */
+/**
+ * Validate ONE audit subject, degrading if the filesystem refuses it.
+ *
+ * THE boundary guard, and deliberately the only one of its kind. The first
+ * version of this fix guarded the directory walk alone, which left every other
+ * way into a validator unprotected: a `SKILL.md` named directly on the command
+ * line, a plugin directory, a marketplace, each surface of a multi-surface tree.
+ * All of them still ended the whole run with `status: error`, exit 2 and zero
+ * findings — the exact symptom of issue #180, in the lanes nobody had checked.
+ *
+ * Guarding the seven dispatch sites individually would have been the same mistake
+ * a seventh time. This function is what every one of them is reached through, so
+ * it is where "the environment refused this subject" becomes a finding instead of
+ * an abort. It is also the recursion point — `recurseIntoMarketplacePlugins` and
+ * the `--user` target loop both re-enter here — so an unreadable plugin costs its
+ * own subject and nothing else.
+ *
+ * The walk keeps its own per-entry guard: this one would answer at whole-subject
+ * granularity, discarding findings already collected from readable siblings, and
+ * degrading as narrowly as possible is the entire point.
+ */
 export declare function getValidationResults(scanPath: string, recursive: boolean, options: AuditCommandOptions, logger: ReturnType<typeof createLogger>, locationRoot: string): Promise<ValidationResult[]>;
 /**
  * Run compatibility analysis on plugin results and return a map of path -> CompatibilityResult.

package/dist/commands/audit.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"audit.d.ts","sourceRoot":"","sources":["../../src/commands/audit.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAMH,OAAO,EAgBL,KAAK,oBAAoB,EAIzB,KAAK,gBAAgB,EACtB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EAYL,KAAK,mBAAmB,EACxB,KAAK,iBAAiB,EAEvB,MAAM,wCAAwC,CAAC;AAEhD,OAAO,EAGL,KAAK,cAAc,EAEpB,MAAM,4BAA4B,CAAC;AAapC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAuBpC,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAyBlD,MAAM,WAAW,mBAAmB;IAClC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC5B,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,qBAAqB,CAAC,EAAE,OAAO,CAAC;CACjC;AAOD;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC,6FAA6F;IAC7F,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAC;CACjD;AAqQD;;;GAGG;AACH,wBAAgB,kBAAkB,IAAI,OAAO,CA8I5C;AAGD;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAgB,eAAe,CAAC,UAAU,EAAE,SAAS,MAAM,EAAE,EAAE,SAAS,EAAE,OAAO,GAAG,MAAM,EAAE,CAM3F;AAkED;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,cAAc,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAKzD;AAqMD;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CACpC,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,mBAAmB,EAC5B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,UAAU,CAAC,OAAO,YAAY,CAAC,GACtC,OAAO,CAAC;IACT,OAAO,EAAE,gBAAgB,EAAE,CAAC;IAC5B,QAAQ,EAAE,UAAU,CAAC,OAAO,gBAAgB,CAAC,CAAC;CAC/C,CAAC,CAqDD;AAsDD,wBAAsB,YAAY,CAChC,UAAU,EAAE,MAAM,GAAG,SAAS,EAC9B,OAAO,EAAE,mBAAmB,GAC3B,OAAO,CAAC,IAAI,CAAC,CAiCf;AAmKD;;;;;;;;;GASG;AACH;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,wBAAsB,oBAAoB,CACzC,QAAQ,EAAE,MAAM,EAChB,SAAS,EAAE,OAAO,EAClB,OAAO,EAAE,mBAAmB,EAC5B,MAAM,EAAE,UAAU,CAAC,OAAO,YAAY,CAAC,EACvC,YAAY,EAAE,MAAM,GAClB,OAAO,CAAC,gBAAgB,EAAE,CAAC,CAU7B;AAoMD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,iBAAiB,CACrC,OAAO,EAAE,gBAAgB,EAAE,EAC3B,MAAM,EAAE,UAAU,CAAC,OAAO,YAAY,CAAC,EACvC,YAAY,EAAE,MAAM,EACpB,iBAAiB,CAAC,EAAE,iBAAiB,EACrC,UAAU,GAAE,iBAAiB,GAAG,IAAW,GAC1C,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,mBAAmB,CAAC,CAAC,CAiC3C;AAmFD,iBAAS,gBAAgB,CACvB,OAAO,EAAE,gBAAgB,EAAE,EAC3B,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,GAAG,CAAC,MAAM,EAAE,mBAAmB,CAAC,GAAG,SAAS,EACvD,OAAO,EAAE,OAAO,EAChB,IAAI,EAAE,MAAM;;wBAhDgC,mBAAmB;;YA8iCvD,MAAM;aACL,gBAAgB;iBACZ,cAAc;cACjB,MAAM;;EAv/BjB;AAkLD;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmCG;AACH,wBAAgB,wBAAwB,CACtC,OAAO,EAAE,SAAS,gBAAgB,EAAE,EACpC,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,OAAO,GACf,MAAM,EAAE,CA4BV;AAwXD;;;;;GAKG;AACH,wBAAgB,gBAAgB,IAAI,IAAI,CAOvC;AAkUD;;;;;;GAMG;AACH,UAAU,gBAAgB;IACxB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,eAAe,EAAE,MAAM,CAAC;CACzB"}

package/dist/commands/audit.js

@@ -5,11 +5,11 @@
 import * as fs from 'node:fs';
 import { existsSync as fsExistsSync } from 'node:fs';
 import { basename } from 'node:path';
-import { calculateValidationStatus, countBySeverity, } from '@vibe-agent-toolkit/agent-schema';
-import { crawlAndResolveRegistry, detectDeclaredButMissing, detectMarketplacePluginSourceMissing, resetPackagingRegistryCache, detectPresentButUndeclared, detectReferenceTargetMissing, detectResourceFormat, enumerateSurfaces, validate, validateMarketplace, validateSkill, validateSkillForPackaging, } from '@vibe-agent-toolkit/agent-skills';
+import { crawlAndResolveRegistry, detectDeclaredButMissing, detectMarketplacePluginSourceMissing, resetPackagingRegistryCache, detectPresentButUndeclared, detectReferenceTargetMissing, detectResourceFormat, enumerateSurfaces, materializeIssue, validate, validateMarketplace, validateSkill, validateSkillForPackaging, } from '@vibe-agent-toolkit/agent-skills';
 import { analyzeCompatibility, checkSettingsCompatibility, detectSkillClaudePluginNameMismatch, crawlSkillLinkRegistry, extractClaudeMarketplaceInventory, extractClaudePluginInventory, getClaudeUserPaths, readEffectiveSettings, validatePlugin, } from '@vibe-agent-toolkit/claude-marketplace';
 import { detectFormat } from '@vibe-agent-toolkit/discovery';
-import { findProjectRoot, gitFindRoot, isAbsolutePath, isGitUrl, issueLocation, parseGitUrl, resetProjectRootCaches, safePath, } from '@vibe-agent-toolkit/utils';
+import { calculateValidationStatus, countBySeverity, } from '@vibe-agent-toolkit/schema';
+import { findProjectRoot, gitFindRoot, isAbsolutePath, isFilesystemAccessError, isGitUrl, issueLocation, parseGitUrl, resetProjectRootCaches, safePath, } from '@vibe-agent-toolkit/utils';
 import { Command } from 'commander';
 import picomatch from 'picomatch';
 import { resetSkillDiscoveryCache, resolveProjectDeclaredEvalSuites, resolveSkillPackagingConfig, stripValidationAllowForDisplay, } from '../skill-resolution/packaging-config.js';
@@ -592,6 +592,13 @@ function applySeverityFilter(results, config) {
     }
     const skillsConfig = config.skills;
     const defaultSeverity = skillsConfig.defaults?.validation?.severity ?? {};
+    // `.filter` after `.map`, not `.map` alone: a synthetic unreadable-path result
+    // exists ONLY to carry its finding, so once the adopter has set
+    // `severity.SCAN_PATH_UNREADABLE: ignore` the result has nothing left to say.
+    // Keeping it published `status: success` for a path the scan never read — the
+    // report positively asserting that an unread path PASSED, which is a stronger
+    // falsehood than the count inflation noted on `unreadablePathResult`. Dropping
+    // it is what "ignore" already means everywhere else.
     return results.map(result => {
         const skillName = SKILL_RESULT_TYPES.has(result.type) ? result.metadata?.name : undefined;
         const perSkillSeverity = skillName === undefined
@@ -614,7 +621,21 @@ function applySeverityFilter(results, config) {
             return result;
         }
         return buildFilteredResult(result, resolvedIssues);
-    });
+    }).filter(result => !isEmptiedUnreadablePathResult(result));
+}
+/**
+ * A synthetic unreadable-path result whose only finding was ignored away.
+ *
+ * Keyed on the shape this module itself produces — `type: 'unknown'`, no
+ * metadata, and now no issues — rather than on a marker field, because
+ * `ValidationResult` is a shared contract and this is the one producer that needs
+ * to be recognised. A genuinely-unknown resource from `unified-validator` carries
+ * metadata or issues and is unaffected.
+ */
+function isEmptiedUnreadablePathResult(result) {
+    return result.type === 'unknown'
+        && result.issues.length === 0
+        && result.metadata === undefined;
 }
 /**
  * Resolve `--settings`-driven EffectiveSettings if both --settings and
@@ -649,7 +670,30 @@ export async function buildAuditReport(scanPath, options, startTime, logger) {
     const scanRoot = deriveScanRoot(scanPath);
     const rawResults = await getValidationResults(scanPath, recursive, options, logger, scanRoot);
     // Load config for severity filtering (audit ignores allow; only severity matters).
-    const config = loadConfig(deriveConfigRoot(scanPath));
+    //
+    // Guarded, and the ordering is why: the scan above has ALREADY run and collected
+    // every finding by this point. An unreadable or malformed config here threw past
+    // all of it and ended the command with `status: error` and zero findings —
+    // discarding completed work to report a problem with a file that only decides
+    // which findings to *hide*. Every other `loadConfig` in this file is already
+    // wrapped for the same reason; this one was missed.
+    //
+    // Falling back to no config means no severity overrides are applied, so findings
+    // are reported at their default severity. That is the safe direction: it can
+    // only show more than the adopter asked for, never less.
+    let config;
+    try {
+        config = loadConfig(deriveConfigRoot(scanPath));
+    }
+    catch (err) {
+        // `warn`, not `debug`. Falling back to no config is the safe direction — it
+        // can only show more than the adopter asked for, never less — but it means
+        // every `validation.severity` override they wrote is silently inert. Before
+        // this guard the command failed loudly and told them; degrading without a word
+        // would trade a crash for a config that quietly stopped working, which is the
+        // harder problem to notice.
+        logger.warn(`Config could not be read; severity overrides are not applied: ${String(err)}`);
+    }
     // Apply severity filtering: hide codes whose effective severity is 'ignore'.
     // Allow is deliberately NOT applied — audit is advisory only.
     const results = applySeverityFilter(rawResults, config);
@@ -788,7 +832,7 @@ async function runInventoryDetectors(scanPath, type, locationRoot, prebuiltInv)
         ];
     }
     if (type === 'marketplace') {
-        const inv = prebuiltInv?.kind === 'marketplace' ? prebuiltInv : await extractClaudeMarketplaceInventory(scanPath);
+        const inv = prebuiltInv?.kind === 'marketplace' ? prebuiltInv : await extractClaudeMarketplaceInventory(scanPath, { gitTrackerSource: gitTrackerForProjectRoot });
         return detectMarketplacePluginSourceMissing(inv, locationRoot);
     }
     return [];
@@ -869,7 +913,41 @@ function appendInventoryParseErrors(result, inv, locationRoot) {
  *   location reads, or a run spanning several configs emits one document in
  *   several coordinate systems. Recursion passes it through unchanged.
  */
+/**
+ * Validate ONE audit subject, degrading if the filesystem refuses it.
+ *
+ * THE boundary guard, and deliberately the only one of its kind. The first
+ * version of this fix guarded the directory walk alone, which left every other
+ * way into a validator unprotected: a `SKILL.md` named directly on the command
+ * line, a plugin directory, a marketplace, each surface of a multi-surface tree.
+ * All of them still ended the whole run with `status: error`, exit 2 and zero
+ * findings — the exact symptom of issue #180, in the lanes nobody had checked.
+ *
+ * Guarding the seven dispatch sites individually would have been the same mistake
+ * a seventh time. This function is what every one of them is reached through, so
+ * it is where "the environment refused this subject" becomes a finding instead of
+ * an abort. It is also the recursion point — `recurseIntoMarketplacePlugins` and
+ * the `--user` target loop both re-enter here — so an unreadable plugin costs its
+ * own subject and nothing else.
+ *
+ * The walk keeps its own per-entry guard: this one would answer at whole-subject
+ * granularity, discarding findings already collected from readable siblings, and
+ * degrading as narrowly as possible is the entire point.
+ */
 export async function getValidationResults(scanPath, recursive, options, logger, locationRoot) {
+    try {
+        return await validateAuditSubject(scanPath, recursive, options, logger, locationRoot);
+    }
+    catch (error) {
+        // Only the filesystem refusing the subject degrades; a defect in a validator
+        // must still fail loudly rather than be reported as a permissions problem.
+        if (!isFilesystemAccessError(error))
+            throw error;
+        logger.debug(`Unreadable audit subject: ${scanPath}`);
+        return [unreadablePathResult(scanPath, error, locationRoot)];
+    }
+}
+async function validateAuditSubject(scanPath, recursive, options, logger, locationRoot) {
     const format = detectFormat(scanPath);
     // Special handling for direct SKILL.md file
     if (format === RESOURCE_TYPE_AGENT_SKILL) {
@@ -923,7 +1001,7 @@ export async function getValidationResults(scanPath, recursive, options, logger,
             // recursion into co-located, path-source plugins. discovered.plugins[]
             // is populated only for path sources that exist on disk (git/npm/unknown
             // sources are declarations only and stay out of scope).
-            const marketplaceInv = await extractClaudeMarketplaceInventory(scanPath);
+            const marketplaceInv = await extractClaudeMarketplaceInventory(scanPath, { gitTrackerSource: gitTrackerForProjectRoot });
             const marketplaceInventoryIssues = await runInventoryDetectors(scanPath, 'marketplace', locationRoot, marketplaceInv);
             appendIssues(result, marketplaceInventoryIssues);
             logger.debug(`Inventory detectors emitted ${marketplaceInventoryIssues.length.toString()} issues for marketplace at ${scanPath}`);
@@ -972,9 +1050,26 @@ async function validatePluginSkillsViaInventory(scanPath, options, logger, locat
             continue;
         }
         logger.debug(`  Validating plugin-bundled skill (inventory): ${skill.files.skillMd}`);
-        // No crawl: `validatePlugin` already scanned the whole plugin tree, nested
-        // skill directories included, so this lane would duplicate its findings.
-        results.push(await validateSingleSkill(skill.files.skillMd, options, logger, locationRoot, false));
+        // Guarded PER SKILL, not left to the boundary. The boundary guard answers at
+        // whole-subject granularity, so one unreadable bundled `SKILL.md` discarded
+        // the plugin's own manifest findings and every readable sibling skill with
+        // it — 4 results down to 1 — and anchored the finding at the plugin root,
+        // which is perfectly readable. That contradicted this code's own promise
+        // that an unreadable path "costs its own subject and nothing else", and the
+        // documented promise that "a skill beside the unreadable path is validated
+        // exactly as if it were not there". Degrading as narrowly as the structure
+        // allows is the whole point; here the skill is the unit.
+        try {
+            // No crawl: `validatePlugin` already scanned the whole plugin tree, nested
+            // skill directories included, so this lane would duplicate its findings.
+            results.push(await validateSingleSkill(skill.files.skillMd, options, logger, locationRoot, false));
+        }
+        catch (error) {
+            if (!isFilesystemAccessError(error))
+                throw error;
+            logger.debug(`  Unreadable plugin-bundled skill: ${skill.files.skillMd}`);
+            results.push(unreadablePathResult(skill.files.skillMd, error, locationRoot));
+        }
     }
     return results;
 }
@@ -1590,7 +1685,12 @@ async function getOrCreateInventoryRegistry(projectRoot) {
  */
 async function pluginInventoryAt(dir) {
     const projectRoot = findProjectRoot(dir);
-    return extractClaudePluginInventory(dir, projectRoot === null ? undefined : () => getOrCreateInventoryRegistry(projectRoot), gitTrackerForProjectRoot);
+    return extractClaudePluginInventory(dir, {
+        ...(projectRoot === null
+            ? {}
+            : { sharedRegistry: () => getOrCreateInventoryRegistry(projectRoot) }),
+        gitTrackerSource: gitTrackerForProjectRoot,
+    });
 }
 /**
  * Reset all module-level audit caches. Must be called at the start of every
@@ -1667,6 +1767,93 @@ function getSkipReason(entry, fullPath, gitIgnoredMap, excludeMatchers) {
     }
     return null;
 }
+/**
+ * The one finding a path the walk could not read produces — a directory it could
+ * not enter, or a file it could not open.
+ *
+ * A synthetic result rather than an issue appended to some neighbour: nothing
+ * about the unreadable path was validated, so it has no host result to hang
+ * off, and attaching it to a sibling would attribute the condition to a tree that
+ * scanned fine. Typed `unknown` for the same reason — the whole point is that its
+ * contents were never seen, so any more specific type would be a claim the scan
+ * cannot support.
+ *
+ * The OS message is carried through verbatim (it names the errno and the syscall,
+ * which is what distinguishes a permissions problem from a vanished mount), but it
+ * is no longer the ONLY thing the run says — the code, the location and the fix
+ * come from the registry.
+ *
+ * KNOWN, and deliberately not fixed here: this result counts toward
+ * `summary.filesScanned`, so a path the scan could not read is counted among the
+ * files it scanned. Dropping it from that denominator alone would be worse —
+ * `filesWithWarnings` counts the same results, so the summary would report more
+ * files with warnings than files scanned. Saying it honestly needs a field of its
+ * own, which is a change to the report's shape and belongs with issue #177
+ * ("report counts don't describe the artifact") rather than smuggled in here. The
+ * finding itself names the path, so nothing is hidden in the meantime.
+ */
+function unreadablePathResult(dirPath, error, locationRoot) {
+    // `issueLocation` is `path.relative`, so it answers `''` when the subject IS the
+    // anchor — and for this finding that is not exotic, it is `vat audit <path>`
+    // where the named path is the unreadable one. `''` reached the report as
+    // `location: ""` and rendered the detail as a bare `": EACCES …"`. `.` is that
+    // same path spelled as something a reader can act on. The identical fix, for the
+    // identical reason, already exists on the distributed-tree finding — see
+    // `anchoredTreeLocation` in ./audit/distributed-tree.ts.
+    const location = issueLocation(dirPath, locationRoot) || '.';
+    const issues = [
+        materializeIssue('SCAN_PATH_UNREADABLE', {
+            location,
+            detail: `${location}: ${error instanceof Error ? error.message : String(error)}`,
+        }),
+    ];
+    const issueCounts = countBySeverity(issues);
+    return {
+        path: dirPath,
+        type: 'unknown',
+        status: calculateValidationStatus(issues),
+        summary: formatCountsSummary(issueCounts),
+        issues,
+        issueCounts,
+    };
+}
+/**
+ * Scan ONE directory entry, degrading to a finding if the filesystem refuses it.
+ *
+ * Guarded per ENTRY, not just per directory: wrapping only the parent `readdir`
+ * left the other half of the same defect live — an unreadable FILE (a root-owned
+ * `SKILL.md`, a quarantined bundle) threw out of `validateSkill` and still
+ * aborted the whole run with `status: error` and zero findings. Under
+ * `~/.claude/plugins` — the flagship `vat audit --user` target, populated by sudo
+ * installs and macOS quarantine — a root-owned FILE is at least as likely as a
+ * root-owned directory (issue #180).
+ *
+ * Extracted from `scanDirectory` rather than inlined because the added branch put
+ * that function over the cognitive-complexity ceiling; the walk keeps the
+ * bookkeeping, this keeps the per-entry decision.
+ */
+async function scanEntry(entry, fullPath, ctx) {
+    try {
+        if (entry.isFile()) {
+            const result = await handleFileEntry(entry, fullPath, ctx.options, ctx.logger, ctx.scanCtx);
+            return result === null ? [] : [result];
+        }
+        if (entry.isDirectory()) {
+            return await handleDirectoryEntry(fullPath, ctx.recursive, ctx.options, ctx.logger, ctx.baseDir, ctx.descendCtx, ctx.nestedConfigLog);
+        }
+        return [];
+    }
+    catch (error) {
+        // ONLY filesystem-access errors degrade. Anything else is rethrown, because
+        // turning a genuine VAT bug into a `warning` about the file it happened on is
+        // the same "detector silently disables itself" shape this guard exists to
+        // prevent — it would make the tool quietest exactly when it is most wrong.
+        if (!isFilesystemAccessError(error))
+            throw error;
+        ctx.logger.debug(`Unreadable entry: ${fullPath}`);
+        return [unreadablePathResult(fullPath, error, ctx.scanCtx.locationRoot)];
+    }
+}
 async function scanDirectory(dirPath, recursive, options, logger, scanCtx, baseDir, nestedConfigLog) {
     const fs = await import('node:fs/promises');
     const results = [];
@@ -1708,7 +1895,24 @@ async function scanDirectory(dirPath, recursive, options, logger, scanCtx, baseD
     if (resolvedScanCtx.projectExcludes !== null) {
         excludeMatchers.push(resolvedScanCtx.projectExcludes);
     }
-    const entries = await fs.readdir(dirPath, { withFileTypes: true });
+    // Guarded because `vat audit` is a bulk linter over trees it does not own, and
+    // an unreadable entry is an ordinary condition there — one root-owned directory
+    // under `~/.claude/plugins` used to abort the flagship `vat audit --user` run
+    // outright, losing every finding already collected (issue #180). The failure is
+    // scoped to the subtree that caused it: this returns instead of throwing, so the
+    // CALLER's loop keeps its readable siblings and the walk continues.
+    let entries;
+    try {
+        entries = await fs.readdir(dirPath, { withFileTypes: true });
+    }
+    catch (error) {
+        // Same predicate as the per-entry guard below — see it for why a non-IO
+        // throw must not be degraded into a finding.
+        if (!isFilesystemAccessError(error))
+            throw error;
+        logger.debug(`Unreadable directory: ${dirPath}`);
+        return [unreadablePathResult(dirPath, error, resolvedScanCtx.locationRoot)];
+    }
     const descendCtx = await contextForDescendants(dirPath, entries, resolvedScanCtx);
     // Build full paths and batch-check gitignore status
     const entryPaths = entries.map(e => safePath.join(dirPath, e.name));
@@ -1720,18 +1924,13 @@ async function scanDirectory(dirPath, recursive, options, logger, scanCtx, baseD
             logger.debug(`Excluding path: ${skipReason}`);
             continue;
         }
-        if (entry.isFile()) {
-            const result = await handleFileEntry(entry, fullPath, options, logger, resolvedScanCtx);
-            if (result !== null) {
-                results.push(result);
-            }
-        }
-        else if (entry.isDirectory()) {
-            // `descendCtx`, not `resolvedScanCtx`: this level's own skill (if any)
-            // owns everything below, including this subdirectory.
-            const dirResults = await handleDirectoryEntry(fullPath, recursive, options, logger, resolvedBaseDir, descendCtx, resolvedNestedLog);
-            results.push(...dirResults);
-        }
+        results.push(...await scanEntry(entry, fullPath, {
+            recursive, options, logger,
+            scanCtx: resolvedScanCtx,
+            descendCtx,
+            baseDir: resolvedBaseDir,
+            nestedConfigLog: resolvedNestedLog,
+        }));
     }
     return results;
 }